Overview

Eighteen more insecticide resistance data from the original IRBase resource are now available in our new Population Biology resource. This will immediately allow new visualizations and will allow building integrated views of genetic, resistance and even pathogen data.

Gene set updates for 7 members of Anopheles cluster based on automatic annotation and comparative approaches.

We are hosting the annotation software Web Apollo, the manual annotations created here will be collected by VectorBase to update the gene sets, you do not need to submit any files to us. As a transition period, during the next two months we will continue to receive GFF3 files for gene annotations generated with softwares such as Artemis.

The Ensembl genome browser has been updated to version 75. New features include the ability to define a region to view/annotate in our new WebApollo instances.

Seven of the tutorials and/or their practice exercises have been updated for this release. Additionally, we are also providing a link to Web Apollo user guide.

Blast, ClustalW, and Hmmer have job numbers locked to the user that created them. Jobs that are created while not logged in will be accessible to anyone until they are deleted periodically by VectorBase. User jobs that are not saved will also be deleted periodically.

Genomes

VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this: ).

Ontologies

Ontology

Version

Description

Changes in this release

GAZ

1.512

A controlled vocabulary of geographic locations.

GO

2014-06-12

The gene ontology.

Updated to the 2014-06-12 daily release.

IDODEN

0.18

Beta release of an an ontology that describes all aspects of Dengue. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and viruses as well as interventions and attempts to control the disease.

IDOMAL

1.36

An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.

MIRO

2.2

An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.

TADS

1.22

An ontology to describe the anatomy of ticks.

TGMA

1.12

An ontology to describe the anatomy of mosquitoes.

Tutorials

Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files.

Known issues

It is not possible to upload files to WebApollo yet, this will get fix in early July.

In memory of VectorBase alumni Dr. Martin Hammond

We dedicate this release of VectorBase to Dr. Martin Hammond, one time outreach officer, VectorBase gene builder and eternally enthusiastic, inquisitive scientist Martin passed away recently after a battle with motor neurone disease. Martin came to EMBL-EBI after many years teaching science at undergraduate level, joining the Ensembl team before becoming instrumental in the Anopheles gambiae project that developed into VectorBase. Post EMBL-EBI he returned to teaching at the University of East Anglia in Norwich. A keen cyclist with a keener mind, he is much missed.

Release date:

Wednesday, June 25, 2014

This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201400029C.